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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactgtattgcatttgattgtttcagtttctcaattagcactgtgctatcaagcattggttttaactacttccatcttacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g21950.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G010823_T01 (Zea mays), 3'ss of exon 11
---gtaagactgt-attgcatt-tgatt--gtttcagtttctcaattagc-----actgtgctatcaagcattggttttaactacttccatcttacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG
      ||||||| |||  ||  ||||   ||||  || | |  || | |     || |   | | |||| |  |||| ||   |||  |  || ||||| |||||||| || ||||||||||||||  |||| ||||||||||| |||
gtaagcagactgttattatatcatgatatggtttttgtatgttgatcaacggaagacagcattgtgaagcttctgtttcaa---cttgtacttttcagGGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA02G01930.1 (Glycine max), 3'ss of exon 11
---------gtaagactgtattgcatttgattgtttcagtttctcaattagcactgtgctatcaagcattggttttaa----ctacttccatct--tacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG
          ||    | || |     | | |    ||    ||   |  |  |  | | ||      |||  | |||    | || |   |||  | ||||| || |||||||| |||||||||||||| ||||| ||||| ||||| |||
accaatcatttatatttttactagggataagttagacaacaccttc-tatgtgccttacaattggagtttgactctaagccacaaccttattctgtttcagGGGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA10G02040.1 (Glycine max), 3'ss of exon 11
-----------------------------------------gtaagactgtattgcatttgattgtttcagtttctcaattagcactg--tgctatcaagcattggttttaactacttccatctta-----cagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG
                                            ||    | |    |||  ||| |  ||||  |   ||     |   | | ||      |||  | |||  ||  |  | ||      ||||| || ||||||||||||||||||||||| ||||| ||||| ||||| |||
gtaagatcctcatgctgactgaatttaaatttgttacacaaaccagttgttttcttttttacttgctatagttcattgttttatttttgttacaattggaatttgactctaagcacaactgtattctgtttcagGGGAAGGTTAACCCTACCCAGTGTGAGGCTTTGACAATGGTGTGTGCCCAG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA02G01920.1 (Glycine max), 3'ss of exon 11
----------------------------------------gtaagactgtattgcatttgattgtttcagtttctcaattagc--actgtgctatcaagcattggttttaa-ctacttccatctta-----cagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG
                                              |||| ||    |   ||| |  ||||  | ||||         ||| ||      |||  | ||| | ||  |  | ||      ||||| || ||||||||||||||||||||||| ||||| ||||| ||||| |||
gtaagatcctcatgctgactgaatataaatttgttacacaaaccagctgttttcttgtcacttgctatagttcattaatttatttgtcttgcaattggaatttgactctaagccacaactgtattctgtttcagGGGAAGGTTAACCCTACCCAGTGTGAGGCTTTGACAATGGTGTGTGCCCAG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagactgta-ttgcatttgattgtttcagtttctcaattagcact-gtgctatcaagcattggttttaactacttccatcttacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG
||| || || | |     ||   | ||      | |   ||  |||| ||  |       ||   ||||   ||  ||  |||  ||||| || || || ||||| ||||||||||||||||| ||||||||||| |||
gtatgaatgcaatcttcctttgctcttctgtccttttctttttcactagttttgattcaaatgaatttt---tatctctttct--cagGGGAAGGTAAATCCTACACAGTGTGAGGCCTTGACTATGGTTTGTGCACAG

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT5G50950.2 (Arabidopsis thaliana), 3'ss of exon 11
-------------------gtaagactgtattgcatttgattgtttcagtttctcaattagcactgtgctatca-agcattggttttaact--actt----ccatcttacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG
                    || |  | |  ||   ||      | | | |   |   || |  |    | ||| ||  || | || || |  | ||    | ||||  |||||||| || || ||||| ||||||||||||||||| |||||||||||||| 
gtatgaatgcaattttttcctatggttcttatgtcctttccctctgcggctctgcctataccttttatttttcatagattttgattcaattgaattttaatctatctctcagGGAAAGGTAAATCCTACACAGTGTGAGGCCTTGACTATGGTTTGTGCTCAA

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 3'ss of exon 12
------------------------------gtaagactgtattgcatttgattgtttcagtttctcaattagcactgtgctatcaagcattggt--tttaactacttccatcttacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG
                               || ||| |||    |  ||||  ||||| || | |      || |  |   |||   |||  |  |||| ||  ||| || |  |||||||| ||||||||||| |||||||||||  | || ||||| |||||||||
gtaaaatcctgatctctttcccatatatttttatgacagtaaaa-agatgatattttcacttgcacttgctacatttaggattcatttattcatcctttagctttttctattt--cagGGAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|66913561|gb|CX100409.1|CX100409
EST:     TTGGTGAACTTATCCTACCTGAAAATGAGCCTGGGAGCAGCATTATGCCT                         GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG
genomic: TTGGTGAACTTATCCTACCTGAAAATGAGCCTGGGAGCAGCATTATGCCTgtaagactgt ... catcttacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 51 (upstream exon), 65 (downstream exon)
Score: 23

CGGCCCCCGATGTGGACTTGGTGAACTTATCCTACCTGAAAATGAGCCTGGGAGCAGCATTATGCCTgtaagactgt ... catcttacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcaattagcactgtgctatcaagcattggttttaactacttccatcttacagGGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG
                                ttttaac  putative branch site (score: 23)
                                         cttccatctt  putative PPT
                                ttttaacta  TA-rich tract